Boolean relationships follow known biology. (a) Gender difference, XIST high ⇒ RPS4Y1 low, male and female genes are not expressed in the same sample. (b) Gender tissue specific, RPS4Y1 low ⇒ ACPP low, prostate cells are from males. (c) Tissue difference, ACPP high ⇒ GABRB1 low, prostate and brain genes are not expressed in the same samples. (d) Development, HOXD3 high ⇒ HOXA13 low, anterior is different from posterior. (e) Differentiation, KIT high ⇒ CD19 low, differentiated B cell is different from hematopoietic stem cell. (f) Co-expression, CDC2 versus CCNB2.